Hello,
I'm trying to run a nMDS on presence/absence data.
I have a species over sites matrix with 450 sites and 186 species, in
similar structure to the matrix varespec shown in this tutorial
http://cc.oulu.fi/~jarioksa/opetus/metodi/vegantutor.pdf.
The only difference is the data is 0/1 and not frequncy.
metaMDS runs fine and i am able to show the sites scores using ordiplot, but
as for species - i can plot the scores but not the labels. This might be
because the item spcies is missing these values. This is my metaMDS object
species item:
$ species : num [1:186, 1:2] -0.0249 -0.11 -0.4334 -0.6566 0.4679 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:2] "MDS1" "MDS2"
..- attr(*, "shrinkage")= Named num [1:2] 0.413 0.24
.. ..- attr(*, "names")= chr [1:2] "MDS1" "MDS2"
..- attr(*, "centre")= Named num [1:2] -0.1466 0.0388
.. ..- attr(*, "names")= chr [1:2] "MDS1" "MDS2"
This is code i ran:
Sps.mds=metaMDS(spp_sites_mat, distance="jaccard", k=2,autotransform=F)
and this is the data matrix:
str(spp_sites_mat)
List of 186
$ ADON.CUPA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ AEGI.GENI: num [1:450] 0 0 0 0 0 1 1 0 1 0 ...
$ AINS.TRAC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ AJUG.CHAM: num [1:450] 0 1 0 0 0 0 0 0 0 0 ...
$ ALCE.ACAU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ALKA.STRI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ALLI.STAM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ALOP.UTRI: num [1:450] 0 1 1 0 0 0 0 0 1 0 ...
$ ALYS.MINU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ANAG.ARVE: num [1:450] 0 0 0 1 0 0 0 0 0 0 ...
$ ANCH.AEGY: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ANDR.TELE: num [1:450] 1 1 0 0 0 0 0 0 1 0 ...
$ ANEM.CORO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ANTH.HEBR: num [1:450] 1 0 0 1 1 0 0 0 0 0 ...
$ ANTH.PSEU: num [1:450] 0 1 1 0 0 0 0 0 0 0 ...
$ ANTI.ORON: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ AREN.LEPT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ARTE.SQUA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASPH.RAMO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.ASTE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.CALL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.HAMO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.PELE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ASTR.TRIB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ATRA.CANC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ AVEN.BARB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ AVEN.STER: num [1:450] 1 1 1 1 0 0 0 0 0 1 ...
$ BELL.FLEX: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ BISC.DIDY: num [1:450] 0 0 0 0 0 0 0 0 0 1 ...
$ BORA.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ BROM.ALOP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ BROM.FASC: num [1:450] 0 0 0 0 1 1 1 1 1 0 ...
$ BROM.LANC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ BROM.SCOP: num [1:450] 0 1 0 1 1 0 0 0 0 0 ...
$ CALE.ARVE: num [1:450] 0 0 1 1 0 0 0 0 0 0 ...
$ CALE.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CAMP.ERIN: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CAMP.HIER: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CAMP.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CART.TENU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CATA.LUTE: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CATA.RIGI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CENT.CROC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CHAE.TRIC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CHIL.IPHI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CHRY.CORO: num [1:450] 0 0 0 0 0 0 0 1 0 0 ...
$ CLYP.JONT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ COMP.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CONV.ALTH: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CORO.SCOR: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CRAS.ALAT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CREP.ASPE: num [1:450] 1 0 0 1 1 0 0 0 0 0 ...
$ CREP.SANC: num [1:450] 0 1 1 0 0 0 0 0 0 0 ...
$ CRUP.CRUP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CUSC.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ CYNO.DACT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ DAUC.CARO: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ DIAN.SP. : num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ECHI.ADEN: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ECHI.JUDA: num [1:450] 0 0 0 0 0 1 0 1 0 1 ...
$ EROD.GRUI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ EROD.MALA: num [1:450] 0 0 0 0 0 1 0 0 0 0 ...
$ EROD.MOSC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ERUC.HISP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ERYN.CRET: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ EUPH.AULA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ EUPH.CHAM: num [1:450] 0 1 0 0 0 0 0 0 1 0 ...
$ EUPH.HELI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ EUPH.OXYO: num [1:450] 0 0 0 1 0 1 0 0 0 0 ...
$ EUPH.PEPL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ FACT.ASCH: num [1:450] 0 0 0 0 0 0 1 0 0 0 ...
$ FERU.COMM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ FILA.CONT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ FILA.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ FILA.PYRA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GAGE.COMM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GALI.DIVA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GALI.JUDA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GALI.SETA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GERA.MOLL: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GERA.ROTU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ GERO.HYBR: num [1:450] 0 1 0 1 1 0 0 0 0 0 ...
$ HEDY.RHAG: num [1:450] 1 0 0 0 0 0 0 0 0 0 ...
$ HELI.ROTU: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ HELI.SALI: num [1:450] 0 0 0 0 1 1 0 0 1 0 ...
$ HIPP.UNIS: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ HIRS.INCA: num [1:450] 0 0 0 1 0 0 0 0 1 1 ...
$ HORD.BULB: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ HORD.SPON: num [1:450] 0 0 0 1 1 0 0 0 0 0 ...
$ HYME.CIRC: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ HYPA.HIRT: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ IRIS.PALA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ ISAT.LUSI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ LAGO.CUMI: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ LATH.APHA: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ LATH.BLEP: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ LATH.HIER: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
$ LATH.MARM: num [1:450] 0 0 0 0 0 0 0 0 0 0 ...
[list output truncated]
- attr(*, "row.names")= int [1:450] 1 2 3 4 5 6 7 8 9 10 ...
I have no idea why are the species names missing, there are no warning. I
only found questions regarding missing species scores, but that doesn't seem
to be the problem here.
Any idea?
Thank's!
Hila
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